Pins digital 0 and 1 are also serial pins. If you use them as digital input-output do not declare and use the serial port.

Pin digital 13 has a LED in series with a 1k resistor solderd on board. You can use this pin as output (the LED will flicker) but as input it depends, it's pulled LOW, so make sure you don't turn on the internal pull up resitor. You can use a push button for example, tied to Vcc.

PWM is just another function of those pins, the primary function is input-output, so you're fine.